Experimental viral evolution at high mutation rate

描述（由申请人提供）：这项工作将研究病毒在持续高突变率下的进化。高突变率的进化预计会通过有害突变的逐步积累来降低种群的适合度；高致死率甚至会导致种群灭绝，这一过程被称为致命突变。这一原理是临床上常用诱变药物治疗病毒感染的基础。在这里，病毒（噬菌体）将在体外以不同的诱变水平生长，并研究这种诱变的进化后果。在Aim 1中，病毒适应度进化将与基于估计的有害突变率和病毒生活史参数预测适应度下降量的模型进行比较。模型的稳健性将通过以下方式进行评估：(i)在预计会导致灭绝的高水平和较低水平之间改变突变率，（ii）进化有重组和没有重组的病毒，以及（iii）研究具有RNA基因组和其他具有DNA基因组的病毒。一项初步研究已经观察到病毒适应性的进化比预测的要高得多（由于病毒适应），在诱变治疗过程中，将特别关注促进病毒适应的因素。在目标2中，将检测诱变治疗后存活的病毒种群有益表型（例如，在抑制剂上生长的能力）的频率升高，以解决失败的致命诱变是否可能以反生产方式加速进化。在Aim 3中，在诱变治疗中幸存下来的病毒种群和从这些种群中分离出来的病毒将在没有诱变的情况下进化。这里的问题是，在停止治疗后，诱变治疗带来的突变负荷将适应度降至野生型水平以下的时间有多长。总的来说，这些研究应该为体内致死性突变的解释和设计工作提供基础。

DESCRIPTION (provided by applicant): This work will investigate the evolution of viruses subjected to a sustained, high mutation rate. Evolution at a high mutation rate is expected to reduce population fitness by the progressive accumulation of deleterious mutations; high rates can even cause population extinction, a process known as lethal mutagenesis. This principle underlies the common use of mutagenic, drugs to treat viral infections clinically. Here, viruses (bacteriophages) will be grown in vitro at different levels of mutagenesis and the evolutionary consequences of that mutagenesis will be studied. In Aim 1, viral fitness evolution will be compared with a model predicting the amount of fitness decline based on the estimated deleterious mutation rate and viral life history parameters. Robustness of the model will be evaluated by (i) varying the mutation rate between high levels expected to cause extinction and lower levels, (ii) evolving viruses with and without recombination, and (iii) studying viruses with RNA genomes and others with DNA genomes. A preliminary study already observed the evolution of much higher viral fitness than predicted (due to viral adaptation), and special attention will be given to the factors contributing to viral adaptation during mutagenic treatment. In Aim 2, populations of viruses surviving mutagenic treatment will be assayed for elevated frequencies of beneficial phenotypes (e.g., ability to grow on inhibitors), to address whether failed lethal mutagenesis might accelerate evolution in counter-productive ways. In Aim 3, viral populations that survived mutagenic treatment and isolates from those populations will be evolved in the absence of mutagenesis. The question here is how long the mutational load from mutagenic treatment will depress fitness below wild-type levels after treatment is stopped. Collectively, these studies should provide a foundation for interpreting and designing efforts at lethal mutagenesis in vivo. PUBLIC HEALTH RELEVANCE: Some antiviral drugs elevate the mutation rate of the virus. It has been proposed that the elevated mutation rate contributes to curing the infection (extinction through 'lethal mutagenesis'), but the mutagenic drugs are often not successful. The work here will investigate the foundations of lethal mutagenesis and whether the elevated mutation rate might instead lead to enhanced viral evolution.